I like what you said about how you speak. E.g., I could say "You get what I'm saying, right?" in a very gentle tone, asking an earnest question, and it might seem polite, or I could say it in an impatient, accusatory tone, and it might be considered rude. Tone is sometimes more important than word choice when it comes to rudeness and politeness.
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J.R.Dec 8 '12 at 12:31

The courteous thing to do is always to portray yourself in a bad light. So don't run the risk of making the other person out to be unintelligent; portray yourself as unclear and let the other person contradict that.

"That's probably as clear as mud" is a customary expression indicating that you have not expressed yourself well. It gives your interlocutor the opportunity to agree (in which case they have not understood) or disagree (in which case you have expressed yourself well).

Other ways exist. "That sounded complicated!" perhaps; or "Did I explain that well?" Focus on what you said, not the other person's understanding of it.